Recombinant DNA technology has made it possible to insert foreign DNA sequences into the genome of an organism, thus, altering the organism's phenotype. The most commonly used plant transformation methods are Agrobacterium infection and biolistic particle bombardment in which transgenes integrate into a plant genome in a random fashion and in an unpredictable copy number. Thus, efforts are undertaken to control transgene integration in plants.
Methods for inserting or modifying a DNA sequence into the genome of a variety of organism have been developed and can involve site-specific integration techniques, which rely on homologous recombination (U.S. Pat. No. 7,102,055 issued on Sep. 5, 2006) or designer endonucleases such as meganucleases, zinc finger nucleases or TALENs (US patent publication 2009-0133152 A1, published May 21, 2009).
While these systems have provided useful techniques for targeted insertion of sequences of interest, there remains a need for identifying more recognition sites for rare cutting double strand break inducing agents and for identifying recognition sites with increased activity towards rare cutting double strand beak inducing agents.